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Each year, growing demand for silver nanoparticles (AgNP) contributes to the search for alternative methods of their production. Stable AgNP with antibacterial properties, low toxicity to the environment and living organisms are especially valued. In the study presented here, an attempt was made to assess the toxicity of two AgNP solutions produced using the HVAD method to the Chinchilla lanigera genome. The AgNO3 solution was the indicator and reference for the harmfulness of AgNP. The study was carried out in vitro on bone marrow cells isolated from Chinchilla lanigera bones. The genotoxicity was assessed by comet assay, following the treatment of cells with three silver solutions: unstable and sodium citrate-stabilized silver nanoparticles, as well as silver nitrate at three concentrations (5, 10 and 20 µg/L), after 3, 6 and 24 h. Based on the percentage of the DNA content in the comet tail and the tail moment, an increase in cell DNA integrity disruption was demonstrated in all tested variants: of solution, exposure time and concentration, compared to the control sample. A statistically significant correlation was determined between the level of induced DNA breaks and the concentration of the active solutions and the duration of their activity. A solution of silver nanoparticles stabilized with sodium citrate was shown to have the most harmful effect on bone marrow cells. Silver nitrate demonstrated a level of toxicity similar to these particles. Further studies are necessary to directly compare the genotoxic properties of AgNP produced using the HVAD method and the chemical method under the same conditions. [ABSTRACT FROM AUTHOR]

We addressed the spatiotemporal characteristics of four commensal rodent species occurring in Myanmar in comparison with other areas of the Indo-Malayan region. We examined sequence variations of the mitochondrial cytochrome b gene (Cytb) in the Pacific rat (Rattus exulans), roof rat (Rattus rattus complex, RrC), lesser bandicoot rat (Bandicota bengalensis), and house mouse (Mus musculus) using the recently developed time-dependent evolutionary rates of mtDNA. The Cytb sequences of RrC from Myanmar were shown to belong to RrC Lineage II, and their level of genetic diversity was relatively high compared to those of the other three species. RrC was found to have experienced bottleneck and rapid expansion events at least twice in the late Pleistocene period in Myanmar and a nearby region. Accordingly, paleoclimatic environmental fluctuations were shown to be an important factor affecting rodents in the subtropics of the Indo-Malayan region. Our results show that human activities during the last 10,000 years of the Holocene period affected the population dynamics of the rodent species examined, including introducing them to Myanmar from neighboring countries. Further study of these four commensal rodents in other geographic areas of the Indo-Malayan region would allow us to better understand the factors that drove their evolution and their ecological trends. [ABSTRACT FROM AUTHOR]

Background: As the largest group of mammalian species, which are also widely distributed all over the world, rodents are the natural reservoirs for many diverse zoonotic viruses. A comprehensive understanding of the core virome of diverse rodents should therefore assist in efforts to reduce the risk of future emergence or re-emergence of rodent-borne zoonotic pathogens. Results: This study aimed to describe the viral range that could be detected in the lungs of rodents from Mainland Southeast Asia. Lung samples were collected from 3284 rodents and insectivores of the orders Rodentia, Scandentia, and Eulipotyphla in eighteen provinces of Thailand, Lao PDR, and Cambodia throughout 2006–2018. Meta-transcriptomic analysis was used to outline the unique spectral characteristics of the mammalian viruses within these lungs and the ecological and genetic imprints of the novel viruses. Many mammalian- or arthropod-related viruses from distinct evolutionary lineages were reported for the first time in these species, and viruses related to known pathogens were characterized for their genomic and evolutionary characteristics, host species, and locations. Conclusions: These results expand our understanding of the core viromes of rodents and insectivores from Mainland Southeast Asia and suggest that a high diversity of viruses remains to be found in rodent species of this area. These findings, combined with our previous virome data from China, increase our knowledge of the viral community in wildlife and arthropod vectors in emerging disease hotspots of East and Southeast Asia. ADx5T_Q3aYxBw7CRZGTwQ6 Video abstract [ABSTRACT FROM AUTHOR]

The aim of this study is to determine the genetic diversity of species in Rocky mouse, Apodemus mystacinus, using SSR (the simple sequence repeat) loci and to reveal the reasons of this variations, if any. In this study, 69 A. mystacinus samples were studied collected from 18 localities in Turkey. 7 SSR loci were used to determine the genetic diversity of A. mystacinus. As a result of this study, A. mystacinus includes 2 genetic groups that indicate the presence of two subspecies as A. m. mystacinus that is distributed in western Anatolia and A. m. euxinus in eastern Anatolia. This result also supports that one of the micro refugium areas is eastern Turkey and the other western and southern Turkey. [ABSTRACT FROM AUTHOR]

Several rodent lineages independently acquired the ability to dig complex networks of tunnels where fossorial and subterranean species spend part or their whole life, respectively. Their underground lifestyles imposed harsh physiological demands, presumably triggering strong selective pressures on genes involved in energy metabolism like those coding for mitochondrial proteins. Moreover, underground lifestyles must have increased inbreeding and susceptibility to population bottlenecks as well as restricted migration, leading to small effective population size (Ne) that, in turn, must have reduced the effectiveness of selection. These stringent environmental conditions and small Ne might be still operating as antagonist factors of selection efficacy in these rodents. In this report, we tested, in a phylogenetic framework, how the intensity of selection on protein-coding mitochondrial genes (mt-genes) fluctuated along the evolution of fossorial and subterranean rodents respective to aboveground lineages. Our findings showed significant selection relaxation in most mt-genes of subterranean hystricomorphs (African mole-rats, tuco-tucos, and coruro), while only in three mt-genes of fossorial hystricomorphs (degus, red vizcacha rat, and fossorial spiny rats) selection efficacy was strongly reduced, probably due to demographic constraints. Conversely, selection intensification was found to have occurred in three mt-genes in fossorial sciuromorphs (ground squirrels, chipmunks, marmot, and allies). Our findings indicated that evolution of mitogenomes in fossorial and, mainly, in subterranean rodents was a complex output of a balance between intense ecological and physiological pressures, together with demographic constraints leading to genetic drift that, in turn, might have resulted in relaxed selection in hystricomorphs. [ABSTRACT FROM AUTHOR]

Antibody specificity and diversity are generated through the enzymatic splicing of genomic gene segments within each B cell. Antibodies are heterodimers of heavy- and light-chains encoded on separate loci. We studied the antibody repertoire from pooled, splenic tissue of unimmunized, adult female C57BL/6J mice, using high-throughput sequencing (HTS) without amplification of antibody transcripts. We recovered over 90,000 heavy-chain and over 135,000 light-chain immunoglobulin sequences. Individual V-, D-, and J-gene segment usage was uniform among the three mouse pools, particularly in highly abundant gene segments, with low frequency V-gene segments not being detected in all pools. Despite the similar usage of individual gene segments, the repertoire of individual B-cell CDR3 amino acid sequences in each mouse pool was highly varied, affirming the combinatorial diversity in the B-cell pool that has been previously demonstrated. There also was some skewing in the V-gene segments that were detected depending on chromosomal location. This study presents a unique, non-primer biased glimpse of the conventionally housed, unimmunized antibody repertoire of the C57BL6/J mouse. [ABSTRACT FROM AUTHOR]

The Ethiopian highlands are the most extensive complex of mountainous habitats in Africa. The presence of the Great Rift Valley (GRV) and the striking elevational ecological gradients inhabited by recently radiated Ethiopian endemics, provide a wide spectrum of model situations for evolutionary studies. The extant species of endemic rodents, often markedly phenotypically differentiated, are expected to possess complex genetic features which evolved as a consequence of the interplay between geomorphology and past climatic changes. In this study, we used the largest available multi-locus genetic dataset of the murid genus Stenocephalemys (347 specimens from ca 40 localities across the known distributional area of all taxa) to investigate the relative importance of disruptive selection, temporary geographic isolation and introgression in their adaptive radiations in the Pleistocene. We confirmed the four main highly supported mitochondrial (mtDNA) clades that were proposed as four species in a previous pilot study: S. albipes is a sister species of S. griseicauda (both lineages are present on both sides of the GRV), while the second clade is formed by two Afro-alpine species, S. albocaudata (east of GRV) and the undescribed Stenocephalemys sp. A (west of GRV). There is a clear elevational gradient in the distribution of the Stenocephalemys taxa with two to three species present at different elevations of the same mountain range. Surprisingly, the nuclear species tree corresponded only a little to the mtDNA tree. Multispecies coalescent models based on six nuclear markers revealed the presence of six separate gene pools (i.e. candidate species), with different topology. Phylogenetic analysis, together with the geographic distribution of the genetic groups, suggests a complex reticulate evolution. We propose a scenario that involves (besides classical allopatric speciation) two cases of disruptive selection along the elevational ecological gradient, multiple crosses of GRV in dry and cold periods of the Pleistocene, followed by hybridization and mtDNA introgression on imperfect reproductive barriers. Spatial expansion of the currently most widespread “ albipes ” mtDNA clade was followed by population fragmentation, lineage sorting and again by hybridization and mtDNA introgression. Comparison of this genetic structure to other Ethiopian endemic taxa highlight the geographical areas of special conservation concern, where more detailed biodiversity studies should be carried out to prevent many endemic taxa from going extinct even before they are recognized. [ABSTRACT FROM AUTHOR]

Damage to the motor cortex induced by stroke or traumatic brain injury (TBI) can result in chronic motor deficits. For the development and improvement of therapies, animal models which possess symptoms comparable to the clinical population are used. However, the use of experimental animals raises valid ethical and methodological concerns. To decrease discomfort by experimental procedures and to increase the quality of results, non-invasive and sensitive rodent motor tests are needed. A broad variety of rodent motor tests are available to determine deficits after stroke or TBI. The current review describes and evaluates motor tests that fall into three categories: Tests to evaluate fine motor skills and grip strength, tests for gait and inter-limb coordination and neurological deficit scores. In this review, we share our thoughts on standardized data presentation to increase data comparability between studies. We also critically evaluate current methods and provide recommendations for choosing the best behavioral test for a new research line. [ABSTRACT FROM AUTHOR]

Paternal contributions to the zygote are thought to extend beyond delivery of the genome and paternal RNAs have been linked to epigenetic transgenerational inheritance in different species. In addition, sperm-egg fusion activates several downstream processes that contribute to zygote formation, including PLC zeta-mediated egg activation and maternal RNA clearance. Since a third of the preimplantation developmental period in the mouse occurs prior to the first cleavage stage, there is ample time for paternal RNAs or their encoded proteins potentially to interact and participate in early zygotic activities. To investigate this possibility, a bespoke next-generation RNA sequencing pipeline was employed for the first time to characterise and compare transcripts obtained from isolated murine sperm, MII eggs and pre-cleavage stage zygotes. Gene network analysis was then employed to identify potential interactions between paternally and maternally derived factors during the murine egg-to-zygote transition involving RNA clearance, protein clearance and post-transcriptional regulation of gene expression. Our in silico approach looked for factors in sperm, eggs and zygotes that could potentially interact co-operatively and synergistically during zygote formation. At least five sperm RNAs (Hdac11, Fbxo2, Map1lc3a, Pcbp4 and Zfp821) met these requirements for a paternal contribution, which with complementary maternal co-factors suggest a wider potential for extra-genomic paternal involvement in the developing zygote. [ABSTRACT FROM AUTHOR]

Currently, the effects of chronic, continuous low dose environmental irradiation on the mitochondrial genome of resident small mammals are unknown. Using the bank vole ( Myodes glareolus) as a model system, we tested the hypothesis that approximately 50 generations of exposure to the Chernobyl environment has significantly altered genetic diversity of the mitochondrial genome. Using deep sequencing, we compared mitochondrial genomes from 131 individuals from reference sites with radioactive contamination comparable to that present in northern Ukraine before the 26 April 1986 meltdown, to populations where substantial fallout was deposited following the nuclear accident. Population genetic variables revealed significant differences among populations from contaminated and uncontaminated localities. Therefore, we rejected the null hypothesis of no significant genetic effect from 50 generations of exposure to the environment created by the Chernobyl meltdown. Samples from contaminated localities exhibited significantly higher numbers of haplotypes and polymorphic loci, elevated genetic diversity, and a significantly higher average number of substitutions per site across mitochondrial gene regions. Observed genetic variation was dominated by synonymous mutations, which may indicate a history of purify selection against nonsynonymous or insertion/deletion mutations. These significant differences were not attributable to sample size artifacts. The observed increase in mitochondrial genomic diversity in voles from radioactive sites is consistent with the possibility that chronic, continuous irradiation resulting from the Chernobyl disaster has produced an accelerated mutation rate in this species over the last 25 years. Our results, being the first to demonstrate this phenomenon in a wild mammalian species, are important for understanding genetic consequences of exposure to low-dose radiation sources. [ABSTRACT FROM AUTHOR]

The sand rat Psammomys obesus is a gerbil species native to deserts of North Africa and the Middle East, and is constrained in its ecology because high carbohydrate diets induce obesity and type II diabetes that, in extreme cases, can lead to pancreatic failure and death. We report the sequencing of the sand rat genome and discovery of an unusual, extensive, and mutationally biased GC-rich genomic domain. This highly divergent genomic region encompasses several functionally essential genes, and spans the ParaHox cluster which includes the insulin-regulating homeobox gene Pdx1. The sequence of sand rat Pdx1 has been grossly affected by GC-biased mutation, leading to the highest divergence observed for this gene across the Bilateria. In addition to genomic insights into restricted caloric intake in a desert species, the discovery of a localized chromosomal region subject to elevated mutation suggests that mutational heterogeneity within genomes could influence the course of evolution. [ABSTRACT FROM AUTHOR]

Catastrophic natural events can have profound impacts on patterns of genetic diversity. Due to the typically unpredictable nature of such phenomena, however, few studies have been able to directly compare patterns of diversity before and after natural catastrophic events. Here, we examine the impacts of a recent volcanic eruption in southern Chile on genetic variation in the colonial tuco-tuco (Ctenomys sociabilis), a subterranean species of rodent endemic to the area most affected by the June 2011 eruption of the Puyehue-Cordón Caulle volcanic complex. To provide a comparative context for interpreting changes in genetic variation in this species, we also analyze the effects of this eruption on genetic variation in the geographically proximate but more widely distributed Patagonian tuco-tuco (C. haigi). Our analyses indicate that while both C. sociabilis and C. haigi displayed significant post-eruption decreases in population density, the apparent impacts of the eruption on genetic diversity differed between species. In particular, genetic diversity at multiple microsatellite loci increased in C. sociabilis after the eruption while no comparable post-eruption increase in C. haigi was observed at these loci. No changes in post-eruption diversity at the mitochondrial cytochrome b locus were detected for either species. To place these findings in a larger spatiotemporal context, we compared our results for C. sociabilis to genetic data from additional modern and ancient populations of this species. These comparisons, combined with Bayesian serial coalescent modeling, suggest that post-eruption gene flow from nearby populations represents the most probable explanation for the apparent increase in post-eruption microsatellite diversity in C. sociabilis. Thus, detailed comparisons of pre- and post-eruption populations provide important insights into not only the genetic consequences of a natural catastrophic event, but also the demographic processes by which these changes in genetic diversity likely occurred. Los eventos naturales catastróficos pueden generar impactos notables en los patrones de diversidad genética. Debido a que estos fenómenos son típicamente impredecibles, muy pocos estudios han podido dedicarse a comparar patrones de diversidad genética antes y después de un evento natural catastrófico. En este trabajo se examina el impacto de la erupción volcánica en junio de 2011 del complejo volcánico Puyehue-Cordón Caulle sobre la diversidad genética del tuco-tuco colonial (Ctenomys sociabilis), un roedor subterráneo endémico del área más afectada por la erupción volcánica. A su vez, se examinan los efectos de dicha erupción sobre la diversidad genética del parapátrico tuco-tuco patagónico (C. haigi), ampliamente distribuido en el noroeste de Patagonia. Estos análisis indican que, aunque ambas especies muestran un decrecimiento significativo en la densidad poblacional, el impacto de la erupción en la diversidad genética fue diferente entre las especies. Particularmente, en C. sociabilis se observó un aumento de la diversidad genética de varios loci de microsatélites luego de la erupción volcánica, mientras que en C. haigi no se observó tal aumento. Para el locus mitocondrial citocromo b no se observó ningún cambio de diversidad genética luego de la erupción volcánica en ninguna de las especies. Para ubicar estos descubrimientos en un contexto temporal más amplio, los resultados de C. sociabilis se compararon con datos genéticos de otras poblaciones actuales y antiguas de esta especie. Utilizando modelos bayesianos basados en la teoría serial coalescente, esto análisis sugieren que el flujo genético post-erupción representa la explicación más probable al aumento en la diversidad de microsatélites en C. sociabilis. De esta manera, las comparaciones entre poblaciones pre- y post-erupción proporcionan información relevante no solo sobre las consecuencias genéticas de eventos naturales catastróficos, sino también sobre los procesos demográficos que probablemente generaron tales cambios en la diversidad genética. [ABSTRACT FROM AUTHOR]

Agricultural ecosystems are spatially and temporally dynamic systems that support wildlife populations in addition to food production for humans. The composition and configuration of land cover within agricultural systems, which often varies seasonally or annually, can have profound impacts on biodiversity. Specifically, landscape structure can influence animal dispersal and distribution. Depending on species-specific ecology, dispersal may be restricted, resulting in smaller, reproductively isolated populations. Few studies have characterized the spatial genetic structure of small mammal species in agricultural landscapes, despite their importance to crop pest management and food webs within agroecosystems. We characterized the spatial genetic structure of 2 co-distributed Peromyscus species (Peromyscus leucopus and Peromyscus maniculatus bairdii), and quantified relationships between spatial genetic structure based on interindividual relatedness resolved from 10 microsatellite loci, and landscape features hypothesized to influence dispersal. We found significant spatial autocorrelation in interindividual relatedness over interindividual distances of 1,800 m for P. leucopus and 300 m for P. maniculatus bairdii. We also identified distinct genetic clusters of interbreeding individuals for both species. Spatial genetic structure of P. leucopus was significantly related to the distribution of roads, indicating that highly fragmented landscapes could negatively affect dispersal and gene flow. Given the large and growing footprint of agriculture globally, it is important that studies of the effects that landscape features have on dispersal of wildlife species include human-dominated landscapes. [ABSTRACT FROM AUTHOR]

Existing assays of social interaction are suboptimal, and none measures propinquity, the tendency of rodents to maintain close physical proximity. These assays are ubiquitously performed using inbred mouse strains and mutations placed on inbred genetic backgrounds. We developed the automatable tube cooccupancy test (TCOT) based on propinquity, the tendency of freely mobile rodents to maintain close physical proximity, and assessed TCOT behavior on a variety of genotypes and social and environmental conditions. In outbred mice and rats, familiarity determined willingness to cooccupy the tube, with siblings and/or cagemates of both sexes exhibiting higher cooccupancy behavior than strangers. Subsequent testing using multiple genotypes revealed that inbred strain siblings do not cooccupy at higher rates than strangers, in marked contrast to both outbred and rederived wild mice. Mutant mouse strains with "autistic-like" phenotypes (Fmr1-/y and Eif4e Ser209Ala) displayed significantly decreased cooccupancy. [ABSTRACT FROM AUTHOR]

Understanding both the role of selection in driving phenotypic change and its underlying genetic basis remain major challenges in evolutionary biology. Here, we use modern tools to revisit a classic system of local adaptation in the North American deer mouse, Peromyscus maniculatus, which occupies two main habitat types: prairie and forest. Using historical collections, we find that forest-dwelling mice have longer tails than those from nonforested habitat, even when we account for individual and population relatedness. Using genome-wide SNP data, we show that mice from forested habitats in the eastern and western parts of their range form separate clades, suggesting that increased tail length evolved independently. We find that forest mice in the east and west have both more and longer caudal vertebrae, but not trunk vertebrae, than nearby prairie forms. By intercrossing prairie and forest mice, we show that the number and length of caudal vertebrae are not correlated in this recombinant population, indicating that variation in these traits is controlled by separate genetic loci. Together, these results demonstrate convergent evolution of the long-tailed forest phenotype through two distinct genetic mechanisms, affecting number and length of vertebrae, and suggest that these morphological changes-either independently or together-are adaptive. [ABSTRACT FROM AUTHOR]

In natural populations, quantitative trait dynamics often do not appear to follow evolutionary predictions. Despite abundant examples of natural selection acting on heritable traits, conclusive evidence for contemporary adaptive evolution remains rare for wild vertebrate populations, and phenotypic stasis seems to be the norm. This so-called “stasis paradox” highlights our inability to predict evolutionary change, which is especially concerning within the context of rapid anthropogenic environmental change. While the causes underlying the stasis paradox are hotly debated, comprehensive attempts aiming at a resolution are lacking. Here, we apply a quantitative genetic framework to individual-based long-term data for a wild rodent population and show that despite a positive association between body mass and fitness, there has been a genetic change towards lower body mass. The latter represents an adaptive response to viability selection favouring juveniles growing up to become relatively small adults, i.e., with a low potential adult mass, which presumably complete their development earlier. This selection is particularly strong towards the end of the snow-free season, and it has intensified in recent years, coinciding which a change in snowfall patterns. Importantly, neither the negative evolutionary change, nor the selective pressures that drive it, are apparent on the phenotypic level, where they are masked by phenotypic plasticity and a non causal (i.e., non genetic) positive association between body mass and fitness, respectively. Estimating selection at the genetic level enabled us to uncover adaptive evolution in action and to identify the corresponding phenotypic selective pressure. We thereby demonstrate that natural populations can show a rapid and adaptive evolutionary response to a novel selective pressure, and that explicitly (quantitative) genetic models are able to provide us with an understanding of the causes and consequences of selection that is superior to purely phenotypic estimates of selection and evolutionary change. [ABSTRACT FROM AUTHOR]

Allactaga sibirica (Dipodidae) is widely distributed in the northwestern arid regions of China. The complete mitochondrial genome (mitogenome) of A. sibirica was 16,685 bp in length; included 13 protein-coding genes, 2 ribosome genes, 22 tRNA genes, and one control region; and had a structure that was typical of vertebrates. The base composition and codon usage of the mitogenome are described, and the structure of the non-coding sequence in the A. sibirica is reported for the first time. The putative origin of replication for the light strand of A. sibirica was approximately 45 bp long, and was highly conserved in the stem-loop and adjacent sequences. Phylogenetic analyses showed high resolution in each of the main divergent clades within Dipodoidea using mitogenomes data. The results indicated that the Zapodidae group was a representative of very basal taxon in Dipodoidea, and shared a common ancestor with Dipodidae species. Within Dipodidae clade, Allactaginae species was at basal position, and this result was in line with previous molecular systematic and morphological studies. Furthermore, Euchoreutes naso and A. sibirica had a close relationship could implicate a sister-group relationship between Euchoreutinae and Allactaginae. Meanwhile, this work also provided a set of useful data on phylogeny and molecular evolution in Dipodidae species. [ABSTRACT FROM AUTHOR]

The bank vole,Myodes glareolus, lives in deciduous forests throughout the Palearctic region. In Turkey, this species is distributed only in northern Anatolia (the Black Sea region) where these forests exist. This study reveals genetic differentiation among bank vole populations based on two regions of mitochondrial DNA (cytochrome bandD-loop). Populations in northern Anatolia are divided into two genetic lineages (the “eastern” and “western Black Sea” lineages) by the Kızılırmak Valley. While the western Black Sea lineage is close to the Balkan lineage, in accordance with their geographical proximities, surprisingly, the Uludag lineage, also situated in Western Turkey appears related to the eastern Black Sea population. The divergence time analyses suggest a separation between the Balkan and Turkish groups around 0.26 Mya, whereas the split between the eastern and western Black sea lineages appeared a little bit later (0.20 Mya). Our results suggest that regional refuges existed for this species in Turkey and that small-scale habitat fragmentations led to genetic differentiations betweenMyodespopulations. [ABSTRACT FROM AUTHOR]

DNA barcoding has been proposed as a method for species identification. However, this method has been criticised for its over-reliance on a single mitochondrial gene. In this study, four mitochondrial gene regions and one nuclear gene region were used to investigate their different abilities to identify tissue associated with museum specimens ofAethomys chrysophilus,Aethomys ineptusandMicaelamys namaquensis.Aethomys chrysophilusand the more recently elevatedA. ineptusare indistinguishable on morphological grounds; however, their ranges are largely parapatric with only one syntopic locality currently known. All of the mitochondrial gene regions were able to separateM. namaquensisfromA. chrysophilusandA. ineptus, but they varied in their abilities to resolve differences betweenA. chrysophilusandA. ineptus. The sequence results identified a specimen from KwaZulu-Natal that was misclassified and should have been identified asA. ineptus. Seven specimens that had not been reclassified following the elevation ofA. ineptusto species level were identified asA. ineptus. Individuals ofA. chrysophilusfrom Malawi could not be classified as eitherA. chrysophilusorA. ineptus, and may be a hybrid or a new, distinct species. This study indicates that DNA barcoding may be used to separateM. namaquensisfromA. chrysophilusandA. ineptus, and although it was not able to separateA. chrysophilusandA. ineptus, it did indicate specimens from Malawi may be a new cryptic species. [ABSTRACT FROM PUBLISHER]

Background: Genome-wide signatures of convergent evolution are widely expected but rarely revealed in animals. Subterranean rodent genome and transcriptome data produced by next-generation sequencing facilitate the use of phylogenetic methods to infer non-synonymous and synonymous substitution rates within coding regions, which can reveal changes at the molecular level that are correlated with the dramatic shift from a terrestrial to subterranean habitat. Results: Our study used previously sequenced genome or transcriptome data of two subterranean rodents, the blind mole rat and naked mole rat, and their terrestrial relatives, the mouse and guinea pig, to investigate the genetic basis of rodent subterranean adaptation. An analysis of 4996 orthologous genes revealed that the substitution pace of coding sequences was significantly slower in the blind mole rat than in the mouse, and slower in the naked mole rat than in the guinea pig. The dN/dS ratio was significantly higher in the blind mole rat than in the mouse and in the naked mole rat than in the guinea pig. These patterns are most likely related to the longer generation time and lower effective population size of subterranean rodents caused by subterranean ecological constraints. We also identified some genes and gene ontology (GO) categories that might be candidates for adaptation to subterranean life. Conclusions: Our study reveals a case of subterranean convergent evolution in rodents that is correlated with change in the pace and mode of molecular evolution observed at the genome scale. We believe that this genomic signature could have also evolved in other cases of subterranean convergence. Additionally, the genes that displayed the most radical changes in their patterns of evolution and their associated GO categories provide a strong basis for further comparative and functional studies, and potentially reveal molecular signatures of adaptation to subterranean life. [ABSTRACT FROM AUTHOR]

In a paper published in PLoS One and entitled 'Laboratory rodent diets contain toxic levels of environmental contaminants: Implications for regulatory tests', Mesnage et al. (2015) analysed commercial laboratory rodent diets for environmental contaminants and genetically modified organisms (GMOs). In samples from 13 different commercial rodent diets obtained from five continents, the authors of the study report the presence of pesticides, heavy metals, polychlorinated dibenzo-p-dioxins and dibenzofurans, and GMOs. The paper by Mesnage et al. (2015) provides a useful addition to the already existing knowledge in the field. However, there are several limitations with the methodological approach used by the authors, including insufficient information about the test material and methodology used, incomplete reporting of the data, and inappropriate interpretation of legislation and results. The vast majority of pesticides were absent (below the limit of detection), and where detected, the levels of pesticides, heavy metals and dioxins were only just above the limit of detection in the feed samples but below regulatory levels for feed and foodstuffs. Only in a limited number of feed diets did the authors report levels of lead that exceeded the maximum levels specified by legislation for foodstuffs. The application of the ADI concept to claim the existence of a health risk in rodents or to demonstrate background levels of diseases or disorders in rodents has no scientific justification. In an interview conducted with Dr Samsel, the farmwars.info website reports on the presence of glyphosate in three different rodent diets. The information reported on the website is not supported by sufficient detail or a reference to permit a full scientific review. In conclusion, no new scientific elements were provided that would impact on the validity of regulatory feeding tests in the EU. [ABSTRACT FROM AUTHOR]

Compared to humans and other mammals, rodent genomes, specifically Muroidea species, underwent intense chromosome reshuffling in which many complex structural rearrangements occurred. This fact makes them preferential animal models for studying the process of karyotype evolution. Here, we present the first combined chromosome comparative maps between 2 Cricetidae species, Cricetus cricetus and Peromyscus eremicus, and the index species Mus musculus and Rattus norvegicus. Comparative chromosome painting was done using mouse and rat paint probes together with in silico analysis from the Ensembl genome browser database. Hereby, evolutionary events (inter- and intrachromosomal rearrangements) that occurred in C. cricetus and P. eremicus since the putative ancestral Muroidea genome could be inferred, and evolutionary breakpoint regions could be detected. A colocalization of constitutive heterochromatin and evolutionary breakpoint regions in each genome was observed. Our results suggest the involvement of constitutive heterochromatin in karyotype restructuring of these species, despite the different levels of conservation of the C. cricetus (derivative) and P. eremicus (conserved) genomes. © 2015 S. Karger AG, Basel [ABSTRACT FROM AUTHOR]

Genomic resources are important and attainable for examining evolutionary change in divergent natural populations of nonmodel species. We utilized two next-generation sequencing ( NGS) platforms, 454 and SOLi D 5500 XL, to assemble low-coverage transcriptomes of the white-footed mouse ( Peromyscus leucopus), a widespread and abundant native rodent in eastern North America. We sequenced liver m RNA transcripts from multiple individuals collected from urban populations in New York City and rural populations in undisturbed protected areas nearby and assembled a reference transcriptome using 1 080 065 954 SOLi D 5500 XL (75 bp) reads and 3 052 640 454 GS FLX + reads. The reference contained 40 908 contigs with a N50 = 1044 bp and a total content of 30.06 Megabases ( Mb). Contigs were annotated from Mus musculus (39.96% annotated) Uniprot databases. We identified 104 655 high-quality single nucleotide polymorphisms ( SNPs) and 65 single sequence repeats ( SSRs) with flanking primers. We also used normalized read counts to identify putative gene expression differences in 10 genes between populations. There were 19 contigs significantly differentially expressed in urban populations compared to rural populations, with gene function annotations generally related to the translation and modification of proteins and those involved in immune responses. The individual transcriptomes generated in this study will be used to investigate evolutionary responses to urbanization. The reference transcriptome provides a valuable resource for the scientific community using North American Peromyscus species as emerging model systems for ecological genetics and adaptation. [ABSTRACT FROM AUTHOR]

Niviventer is a muroid genus with 17 species widely distributed in East and Southeast Asia. These animals are important components of both extant and fossil small mammal communities, and they are among the most common infectious agents in humans. In this study, we employed partitioned Bayesian and relaxed clock divergence dating analyses and included the Niviventer mitochondrial cytochrome b genes of from GenBank ( n = 223). Although the intra-generic relationships were not fully resolved, we recognized four major clades/subclades that could support further division of the genus. Paraphyletic and polyphyletic species were discovered, and 21 putative species were recognized through species delimitation analysis, which indicated an imperfect taxonomy and the existent of cryptic species. Molecular dating supported Niviventer origination in the late Miocene, and relatively higher diversification rates were observed in the late Pliocene and the Pleistocene, which might correlate with climate fluctuations. [ABSTRACT FROM AUTHOR]

We studied karyotype and chromosomal characteristics of 3 species of five-toed jerboa from central Iran, including Allactaga firouzi, A. williamsi, and A. elater. This study revealed that the 3 species possessed a diploid number of 48 chromosomes. The first pair of chromosomes was significantly larger than other chromosomes in all 3 species. The total length of the haploid genome of Allactaga elater was longer than those of the other 2 species, and most of the chromosomes of the 3 species were metacentric. Based on total form percentage, interchromosomal asymmetry index, and centromeric index, Allactaga elater had the highest interchromosomal asymmetry. Allactaga firouzi showed the highest between-chromosomal symmetry based on the difference of range of relative length, coefficient of variability, and intrachromosomal asymmetry index. Cluster analysis showed that A. firouzi and A. williamsi have more affinity than previously thought. [ABSTRACT FROM AUTHOR]

Retrotransposition is developmentally programmed and such events regulate host genes creating a new trait. A ~120 bp identifier (ID) retroposon insertion was detected in the 161 bp rat c-Ha-ras oncogene far upstream regulatory element. The designed oligonucleotides was probed using gel electrophoresis mobility shift assay to assess transcription factors. The ID retroposon derived Avr1 oligonucleotide binds a nuclear protein complex present in all carcinoma cell lines tested, but not in nuclear extract from normal liver cells. However, Avr2 and Avr3 oligonucleotides (conserved Ha-ras repressor motifs) bind to protein factors found in both normal and carcinoma cells. Also, the Avr3 oligonucleotide binds a small protein in normal cells verses a large complex in carcinoma cells. Each oligonucelotide-protein binding is strong and specific. BLAST sequence analysis has demonstrated that the transposed ID sequence is conserved in too many genes. Avr1 sequence is also a part of the highly expressed HaSV and VL30-retroelements, suggesting that Avr1 factor acts as an activator of transcription. The differential expression of Avr1 trans-activator factor and ubiquitous nature of Avr1 sequence could be used as a marker in cancer diagnostics. This study supports the multiple functions of the smallest ID retroposon shaping the genomic evolution and could be studied further to understand the molecular mechanisms of transposition in cancer, stress and drug resistance. [ABSTRACT FROM AUTHOR]

Abstract: Tuco-tucos (Ctenomys) and related coruros (Spalacopus) are South American subterranean rodents. An energetically demanding lifestyle within the hypoxic, underground atmosphere may change the selective regime on oxidative phosphorylation. We examined whether weak and/or episodic positive directional selection affected the evolution of two mitochondrial genes (COX2, CytB), in a background of purifying selection in these lineages. We estimated rates of synonymous (dS) and non-synonymous (dN) substitutions and found: 1) significantly higher dN/dS ratio in subterranean groups relative to non-subterranean related species, and 2) two codons in each gene under episodic selection: 94 and 277 of COX2 and 269 and 307 of CytB. [Copyright &y& Elsevier]

Ctenomys (tuco-tuco) is the most numerous genus of South American subterranean rodents and one of the most genetically diverse clades of mammals known. In particular, the genus constitutes a very interesting model for evolutionary studies of genetic divergence and conservation. Ctenomys magellanicus is the southernmost species of the group and the only one living in Isla Grande de Tierra del Fuego ( Argentina). This species presents two chromosomal forms ( Cm34 and Cm36) fragmented into demes distributed from the north region (steppe) to the south region (ecotone) of the island, respectively; no hybrids or overlapping areas were detected. To study the historical demography and the spatial genetic structure of the C. magellanicus population we used mitochondrial DNA (mtDNA) (D-loop and cytochrome b) and microsatellite loci. Nine mtDNA haplotypes were identified, three of them belonging to the north and the other six to the south. Shared haplotypes between regions were not detected. mt DNA and microsatellite genotypes showed a marked pattern of population structure with low values of genetic flow between regions. The south is made up of small populations or isolated demes making up an endogamic metapopulation with unique alleles and haplotypes. Also, the results suggest a northward expansion process starting from an ancestral haplotype from the south. That population might have lived at a refuge through the adverse Pleistocene environmental conditions that took place at Tierra del Fuego. Results of this study are relevant to the conservation of C. magellanicus, suggesting that each region (north and south) might be considered as an Evolutionarily Significant Unit. © 2013 The Linnean Society of London [ABSTRACT FROM AUTHOR]

The impact of islanding on the genetics of the dominant species,Niviventer confucianus, was analysed using 13 microsatellite markers. All 16 populations are of high genetic diversity with a total of 134 alleles. The average number of effective alleles (Ne) is 6; the average expected heterozygosity (HE) and polymorphic information content (PIC) are 0.823 and 0.763, respectively. Landscape fragmentation might contribute to weak genetic differentiation among 13 island populations. Values ofFSTsimulated by Structure2.3.4 implied that the 16 populations could be assigned into three clusters, from which we postulated the possible dispersion history. PairwiseFSTtests showed that genetic differences mainly occurred between small island populations and others. Currently, habitat area appears to be the main factor affecting the genetics ofNiviventer confucianus, and not the distances between islands. Hence we suggest that more attention should be paid to habitat area in the future. [ABSTRACT FROM AUTHOR]

Background: The capture and use of disease-related anatomic pathology data for both model organism phenotyping and human clinical practice requires a relatively simple nomenclature and coding system that can be integrated into data collection platforms (such as computerized medical record-keeping systems) to enable the pathologist to rapidly screen and accurately record observations. The MPATH ontology was originally constructed in 2,000 by a committee of pathologists for the annotation of rodent histopathology images, but is now widely used for coding and analysis of disease and phenotype data for rodents, humans and zebrafish. Construction and content: MPATH is divided into two main branches describing pathological processes and structures based on traditional histopathological principles. It does not aim to include definitive diagnoses, which would generally be regarded as disease concepts. It contains 888 core pathology terms in an almost exclusively is_a hierarchy nine layers deep. Currently, 86% of the terms have textual definitions and contain relationships as well as logical axioms to other ontologies such the Gene Ontology. Application and utility: MPATH was originally devised for the annotation of histopathological images from mice but is now being used much more widely in the recording of diagnostic and phenotypic data from both mice and humans, and in the construction of logical definitions for phenotype and disease ontologies. We discuss the use of MPATH to generate cross-products with qualifiers derived from a subset of the Phenotype and Trait Ontology (PATO) and its application to large-scale high-throughput phenotyping studies. MPATH provides a largely species-agnostic ontology for the descriptions of anatomic pathology, which can be applied to most amniotes and is now finding extensive use in species other than mice. It enables investigators to interrogate large datasets at a variety of depths, use semantic analysis to identify the relations between diseases in different species and integrate pathology data with other data types, such as pharmacogenomics. [ABSTRACT FROM AUTHOR]

Background: SV2A, SV2B and SV2C are synaptic vesicle proteins that are structurally related to members of the major facilitator superfamily (MFS). The function and transported substrate of the SV2 proteins is not clearly defined although they are linked to neurotransmitters release in a presynaptic calcium concentration-dependent manner. SV2A and SV2B exhibit broad expression in the central nervous system while SV2C appears to be more restricted in defined areas such as striatum. SV2A knockout mice start to display generalized seizures at a late developmental stage, around post-natal day 7 (P7), and die around P15. More recently, SV2A was demonstrated to be the molecular target of levetiracetam, an approved anti-epileptic drug (AED). The purpose of this work was to precisely analyze and quantify the SV2A, SV2B and SV2C expression during brain development to understand the contribution of these proteins in brain development and their impact on epileptic seizures.Results: First, we systematically analyzed by immunohistofluorescence, the SV2A, SV2B and SV2C expression during mouse brain development, from embryonic day 12 (E12) to P30. This semi-quantitative approach suggests a modulation of SV2A and SV2B expression in hippocampus around P7. This is the reason why we used various quantitative approaches (laser microdissection of whole hippocampus followed by qRT-PCR and western blot analysis) indicating that SV2A and SV2B expression increased between P5 and P7 and remained stable between P7 and P10. Moreover, the increase of SV2A expression in the hippocampus at P7 was mainly observed in the CA1 region while SV2B expression in this region remains stable.Conclusions: The observed alterations of SV2A expression in hippocampus are consistent with the appearance of seizures in SV2A-/- animals at early postnatal age and the hypothesis that SV2A absence favors epileptic seizures around P7. [ABSTRACT FROM AUTHOR]

Clock gene expression is not only confined to the master circadian clock in the suprachiasmatic nucleus (SCN) but is also found in many other brain regions. The phase relationship between SCN and extra-SCN oscillators may contribute to known differences in chronotypes. The Octodon degus is a diurnal rodent that can shift its activity-phase preference from diurnal to nocturnal when running wheels become available. To understand better the relationship between brain clock gene activity and chronotype, we studied the day-night expression of the Period genes, Per1 and Per2, in the SCN and extra-SCN brain areas in diurnal and nocturnal degus. Since negative masking to light and entrainment to the dark phase are involved in the nocturnalism of this species, we also compare, for the first time, Per expression between entrained (EN) and masked nocturnal (MN) degus. The brains of diurnal, MN, and EN degus housed with wheels were collected during the light (ZT4) and dark (ZT16) phases. Per1 and Per2 mRNA levels were analyzed by in situ hybridization. Within the SCN, signals for Per1 and Per2 were higher at ZT4 irrespective of chronotype. However, outside of the SCN, Per1 expression in the hippocampus of EN degus was out of phase (higher values at ZT16) with SCN values. Although a similar trend was seen in MN animals, this day-night difference in Per1 expression was not significant. Interestingly, daily differences in Per1 expression were not seen in the hippocampus of diurnal degus. For other putative brain areas analyzed (cortices, striatum, arcuate, ventromedial hypothalamus), no differences in Per1 levels were found between chronotypes. Both in diurnal and nocturnal degus, Per2 levels in the hippocampus and in the cingulate and piriform cortices were in phase with their activity rhythms. Thus, diurnal degus showed higher Per2 levels at ZT4, whereas in both types of nocturnal degus, Per2 expression was reversed, peaking at ZT16. Together, the present study supports the hypothesis that the mechanisms underlying activity-phase preference in diurnal and nocturnal mammals reside downstream from the SCN, but our data also indicate that there are fundamental differences between nocturnal masked and entrained degus. [ABSTRACT FROM AUTHOR]

Abstract: South American tuco-tucos (Ctenomys) and the related coruro (Spalacopus) are two rodent lineages that have independently colonised the subterranean niche. The energetically demanding lifestyles of these species, coupled with the hypoxic atmospheres characteristic of subterranean environments, may have altered the selective regimes on genes encoding proteins related to cellular respiration. Here, we examined the molecular evolution of 13 protein-coding genes in the mitochondrial genome of seven caviomorph rodents, including these two subterranean genera and their above-ground relatives. Using maximum-likelihood and Bayesian approaches, we estimated rates of synonymous (dS) and nonsynonymous (dN) substitutions. We found a significantly higher ω ratio (dN/dS) in subterranean groups as compared to their non-subterranean counterparts in 11 of 13 genes, although no ω ratio was larger than 1. Additionally, we applied a method based on quantitative physicochemical properties to test for positive selection. Amino acid changes implicated in radical structural or functional shifts in the protein property were found to be ubiquitous across the phylogeny, but concentrated in the subterranean lineages. Convergent changes were also found between the subterranean genera used in this study and other mammals adapted to hypoxia. The results of this study suggest a link between niche shifts and weak directional (or episodic) selection at the molecular level against a background of purifying selection. [Copyright &y& Elsevier]

Adaptation to adverse environmental conditions such as high altitude requires physiological and/or morphological changes. Genome scans provide a means to identify the genetic basis of such adaptations without previous knowledge about the particular genetic variants or traits under selection. In this study, we scanned 3027 amplified fragment length polymorphisms (AFLP) in four populations of the common vole Microtus arvalis for loci associated with local adaptation and high altitude. We investigated voles from two populations at high elevation (∼2000 m a.s.l.) representing the upper limit of the altitudinal distribution of the species and two geographically close low-altitude populations (<600 m a.s.l.). Statistical analysis incorporated a new Bayesian F outlier approach specifically developed for AFLP markers, which considers the intensity of AFLP bands instead of mere presence/absence and allows to derive population-based estimates of allele frequencies and F values. Computer simulations showed that this approach increases the statistical power of the detection of AFLP markers under selection almost to the power of single nucleotide polymorphism (SNP) data without compromising specificity. Our enhanced genome scan resulted in 20 prime candidate markers for positive selection, which show mostly extremely high allele frequency differences between the low- and high-altitude populations. The comparison of global- and pairwise-enhanced genome scans demonstrated further that very strong selective signatures may also be associated with single populations suggesting the importance of local adaptation in alpine populations of common voles. [ABSTRACT FROM AUTHOR]

Aim. The complete mitochondrial genome sequence of a newly discovered vole, Proedromys liangshanensis (Rodentia: Cricetidae: Arvicolinae), was determined. Results. The mitogenome of P. liangshanensis is 16,296  bp in length. As with most other mammals, it contains the same gene order and an identical number of genes or regions, including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one putative control region. The A++T content of the control region is 58.2%, the lowest proportion detected so far in Myomorpha. To confirm the phylogenetic position of P. liangshanensis, we carried out phylogenetic analyses based on complete mitochondrial genomic data using Bayesian, maximum parsimony, and maximum likelihood methods. Conclusion. All results revealed that P. liangshanenis is sister to Microtus. Although the results do not bear light on the validity of the genus Proedromys, based on the morphological characters, we suggest that Proedromys is an independent genus of equal rank to the genus Microtus. [ABSTRACT FROM AUTHOR]

Background: The prairie vole (Microtus ochrogaster) is an emerging rodent model for investigating the genetics, evolution and molecular mechanisms of social behavior. Though a karyotype for the prairie vole has been reported and low-resolution comparative cytogenetic analyses have been done in this species, other basic genetic resources for this species, such as a genetic linkage map, are lacking. Results: Here we report the construction of a genome-wide linkage map of the prairie vole. The linkage map consists of 406 markers that are spaced on average every 7 Mb and span an estimated ∼90% of the genome. The sex average length of the linkage map is 1707 cM, which, like other Muroid rodent linkage maps, is on the lower end of the length distribution of linkage maps reported to date for placental mammals. Linkage groups were assigned to 19 out of the 26 prairie vole autosomes as well as the X chromosome. Comparative analyses of the prairie vole linkage map based on the location of 387 Type I markers identified 61 large blocks of synteny with the mouse genome. In addition, the results of the comparative analyses revealed a potential elevated rate of inversions in the prairie vole lineage compared to the laboratory mouse and rat. Conclusions: A genetic linkage map of the prairie vole has been constructed and represents the fourth genome-wide high-resolution linkage map reported for Muroid rodents and the first for a member of the Arvicolinae sub-family. This resource will advance studies designed to dissect the genetic basis of a variety of social behaviors and other traits in the prairie vole as well as our understanding of genome evolution in the genus Microtus. [ABSTRACT FROM AUTHOR]

Background: Beavers are one of the largest and ecologically most distinct rodent species. Little is known about their evolution and even their closest phylogenetic relatives have not yet been identified with certainty. Similarly, little is known about the timing of divergence events within the genus Castor. Methodology/Principal Findings: We sequenced complete mitochondrial genomes from both extant beaver species and used these sequences to place beavers in the phylogenetic tree of rodents and date their divergence from other rodents as well as the divergence events within the genus Castor. Our analyses support the phylogenetic position of beavers as a sister lineage to the scaly tailed squirrel Anomalurus within the mouse related clade. Molecular dating places the divergence time of the lineages leading to beavers and Anomalurus as early as around 54 million years ago (mya). The living beaver species, Castor canadensis from North America and Castor fiber from Eurasia, although similar in appearance, appear to have diverged from a common ancestor more than seven mya. This result is consistent with the hypothesis that a migration of Castor from Eurasia to North America as early as 7.5 mya could have initiated their speciation. We date the common ancestor of the extant Eurasian beaver relict populations to around 210,000 years ago, much earlier than previously thought. Finally, the substitution rate of Castor mitochondrial DNA is considerably lower than that of other rodents. We found evidence that this is correlated with the longer life span of beavers compared to other rodents. Conclusions/Significance: A phylogenetic analysis of mitochondrial genome sequences suggests a sister-group relationship between Castor and Anomalurus, and allows molecular dating of species divergence in congruence with paleontological data. The implementation of a relaxed molecular clock enabled us to estimate mitochondrial substitution rates and to evaluate the effect of life history traits on it. [ABSTRACT FROM AUTHOR]

Single locus studies might not resolve phylogenetic relationships and the evolutionary history of taxa. The analysis of multiple markers promises higher resolution, and congruence among loci may indicate that the phylogenies represent the underlying species history. Here, we examine the utility of a genome-wide approach based on amplified fragment length polymorphisms (AFLP) and several DNA sequence markers in resolving phylogenetic signals in the rapidly radiating rodent genus Microtus which produced about 70 vole species within the last 1.2–2 myr. The current Holarctic distribution of Microtus is assumed to have resulted from three independent colonization events out of Asia to North America, Europe, and northern Asia without subsequent colonization, which would have led to deep splits between species from different continents. We investigated this hypothesis of three single colonization events by reconstructing the phylogenetic relationships among species from all three continents based on data from the first exon of the nuclear arginine vasopressin receptor 1a gene (EXON1), an adjacent noncoding region and the mitochondrial cytochrome b gene. The phylogenetic patterns obtained from these sequence markers are contrasted to genome-wide data on more than 1800 amplified fragment length polymorphisms (AFLP) analyzed for the same samples. Our results show that the single sequence markers partially resolve the phylogenetic relationships within Microtus, but with some incongruence mostly between EXON1 and the other loci. However, deeper nodes of the radiation are only weakly supported and neither the combination of the markers nor additional nuclear sequences improved the resolution significantly. AFLPs provided much stronger support for major continent-specific clades, and show also that reciprocal monophyly of American and European voles is incomplete. Our results demonstrate that Microtus voles colonized the American and European continents each repeatedly in several independent events on similar colonization routes during their radiation. More generally, this study supports the suitability of AFLPs as an alternative to sequence markers to resolve the evolutionary history of rapidly radiating taxa. [ABSTRACT FROM PUBLISHER]

Multiple Genome Rearrangement (MGR) analysis was used to define the trajectory and pattern of chromosome rearrangement within muroid rodents. MGR was applied using 107 chromosome homologies between Mus, Rattus, Peromyscus, the muroid sister taxon Cricetulus griseus, and Sciurus carolinensis as a non-Muroidea outgroup, with specific attention paid to breakpoint reuse and centromere evolution. This analysis revealed a high level of chromosome breakpoint conservation between Rattus and Peromyscus and indicated that the chromosomes of Mus are highly derived. This analysis identified several conserved evolutionary breakpoints that have been reused multiple times during karyotypic evolution in rodents. Our data demonstrate a high level of reuse of breakpoints among muroid rodents, further supporting the “Fragile Breakage Model” of chromosome evolution. We provide the first analysis of rodent centromeres with respect to evolutionary breakpoints. By analyzing closely related rodent species we were able to clarify muroid rodent karyotypic evolution. We were also able to derive several high-resolution ancestral karyotypes and identify rearrangements specific to various stages of Muroidea evolution. These data were useful in further characterizing lineage-specific modes of chromosome evolution. [ABSTRACT FROM AUTHOR]

The complete mitochondrial genome ofL. edwardsiwas first sequenced and characterized. The genome was 16,284 bases in length and the composition and arrangement of its genes are analogous to most other rodents. The nucleotide sequence date of 12 heavy-strand protein-coding genes ofL. edwardsiand other 26 Muridae species were used for phylogenetic analyses. Trees constructed using Maximum Likelihood, Neighbor Joining and Minimum Evolution demonstrated thatL. edwardsiwas closer to the genus Niviventer than Rattus. Combing previous research, it suggests that Edward’s long-tailed rat is more suitable to be classified into genus Leopoldamys and named asLeopoldamys edwardsi. This study suggested thatR. edwardsiis inappropriate for the other name ofL. edwardsi. [ABSTRACT FROM PUBLISHER]

Abstract: Previous studies have indicated a paucity of SINEs within the genomes of the guinea pig and nutria, representatives of the Hystricognathi suborder of rodents. More recent work has shown that the guinea pig genome contains a large number of B1 elements, expanding to various levels among different rodents. In this work we utilized A–B PCR and screened GenBank with sequences from isolated clones to identify potentially uncharacterized SINEs within the guinea pig genome, and identified numerous sequences with a high degree of similarity (>92%) specific to the guinea pig. The presence of A-tails and flanking direct repeats associated with these sequences supported the identification of a full-length SINE, with a consensus sequence notably distinct from other rodent SINEs. Although most similar to the ID SINE, it clearly was not derived from the known ID master gene (BC1), hence we refer to this element as guinea pig ID-like (GPIDL). Using the consensus to screen the guinea pig genomic database (Assembly CavPor2) with Ensembl BlastView, we estimated at least 100,000 copies, which contrasts markedly to just over 100 copies of ID elements. Additionally we provided evidence of recent integrations of GPIDL as two of seven analyzed conserved GPIDL-containing loci demonstrated presence/absence variants in Cavia porcellus and C. aperea. Using intra-IDL PCR and sequence analyses we also provide evidence that GPIDL is derived from a hystricognath-specific SINE family. These results demonstrate that this SINE family continues to contribute to the dynamics of genomes of hystricognath rodents. [Copyright &y& Elsevier]

The article presents a study that compares the copy number of Short Interspersed Elements (SINEs) or short retroposons, B1 and ID, in rodent genomes. Under the investigation, ID and B1 abundance were studied in rodents that belong to 21 families, and the repetitive DNA sequences were demonstrated in all species that were examined. Result suggests that the entire order of rodents have ID and B1 elements. It also found that retroposition of the elements differ among the genomes of various species.

Earlier, a family of G protein-coupled receptors, termed T2Rs, was identified in the rodent and human genomes through data mining. It was suggested that these receptors mediate bitter taste perception. Analysis of the human genome revealed that the hT2R family is composed of 25 members. However, bitter ligands have been identified for only three human receptors so far. Here we report identification of two novel ligand–receptor pairs. hT2R61 is activated by 6-nitrosaccharin, a bitter derivative of saccharin. hT2R44 is activated by denatonium and 6-nitrosaccharin. Activation profiles for these receptors correlate with psychophysical data determined for the bitter compounds in human studies. Functional analysis of hT2R chimeras allowed us to identify residues in extracellular loops critical for receptor activation by ligands. The discovery of two novel bitter ligand–receptor pairs provides additional support for the hypothesis that hT2Rs mediate a bitter taste response in humans. [ABSTRACT FROM AUTHOR]

Abstract We assessed genome size variation by flow cytometry within and among 31 species of nine families of African and South American hystricognath rodents. Interspecific variation was extensive and genome size was relatively high among the South American radiation whereas only moderate variation and smaller estimates of genome size were observed in the African counterparts. The largest genome size, indicating tetraploidy was recorded in the South American octodontid, Tympanoctomys barrerae (16.8 pg DNA). This quantum shift in DNA content represents a novel mechanism of genome evolution in mammals. As expected in polyploid organisms, varying nucleotypic effects were observed in the dimensions of the sperm cells and lymphocytes of T. barrerae . The role of control mechanisms that influence cell dimensions in polyploid organisms is discussed. [ABSTRACT FROM AUTHOR]

Mysopalacinae (zokors) is a group of fossorial rodents for which the taxonomy has yet to reach consensus. Furthermore, due to their fossorial lifestyle, little is known about their ecology. Molecular data are important to elucidate such aspects. In this paper, the complete mitochondrial DNA genome of Gansu zokor ( Eospalax cansus) of the type found in Lintan, China was determined. The genome is 16,354 bp in length and consists of 13 protein-coding genes, 22 tRNA genes, two ribosomal RNA genes, and two main non-coding regions (the control region and the origin of the light strand replication), the gene composition and order of which are similar to most other mammals. The overall base composition is T 30.0%, C 24.2%, A 33.5%, and G 12.3%, with an A+T bias of 63.5%. These mitogenome sequence data are potentially important for evolutionary, population genetic, and ecological studies of the Mysopalacinae. [ABSTRACT FROM AUTHOR]

While travelling as part of the protected area management activities undertaken by the Instituto Chico Mendes de Conservação da Biodiversidade (ICMBio) in the state of Acre, four records of porcupines (Coendou spp.) were gathered: two for Coendou bicolor and two for Coendou prehensilis. The records for Coendou bicolor are the first for Brazil while the records for Coendou prehensilis present the state of Acre as a potential region of sympatry between C. bicolor and C. prehensilis. [ABSTRACT FROM AUTHOR]

The article presents the author’s view on the question of genetic diversity, based on experiments in toxicological and environmental research and new mouse genetics resources called the Collaborative Cross (CC) and the Diversity Outbred (DO). According to the author, the response to the same dose of chemical or similar environmental exposure are variable, because of genetic differences between people. Comments from professor of biology David Aylor are also included.

The complete mitochondrial genome of Perny's long-nosed squirrel (Dremomys pernyi) was firstly sequenced and characterized. The genome was 16,573 bp in length, and its composition and arrangement of genes were analogous to other rodents. The sequences of 13 protein-coding genes were used to construct phylogenetic tree forD. pernyiand other 13 sciurid species available on GenBank. To date, this is the first species whose complete mitochondrial genome sequence was sequenced in genusDremomys. Our results will provide information for further molecular studies. [ABSTRACT FROM PUBLISHER]

The complete mitochondrial genome of the greater bandicoot rat (Bandicota indica) was first sequenced and characterized. The genome was 16 326 bp in length, the composition and arrangement of its genes were analogous to other rodents. To confirm the phylogenetic position ofB. indica, the mitochondrial nucleotide sequence data of other 20 Rodentia species were used to construct phylogenetic tree by maximum likelihood. Phylogenetic analysis demonstrated that generaBandicotaandRattuswere sister taxa, andB. indicawas closer to the genusRattusthan to generaNiviventerandLeopoldamys. The mitochondrial genome ofB. indicapresented in this study can provide useful information for species delimitation, taxonomic and phylogenetic analyses as well as other studies of the species. [ABSTRACT FROM AUTHOR]